Comparative transcriptomic analyses of powdery mildew resistant and susceptible cultivated cucumber (Cucumis sativus L.) varieties to identify the genes involved in the resistance to Sphaerotheca fuliginea infection

Abstract

Background: Cucumber (Cucumis sativus L.) is a widely cultivated vegetable crop, and its yield and quality are greatly affected by various pathogen infections. Sphaerotheca fuliginea is a pathogen that causes powdery mildew (PM) disease in cucumber. However, the genes involved in the resistance to PM in cucumber are largely unknown.

Methods: In our study, a cucumber PM resistant cultivated variety "BK2" and a susceptible cultivated variety "H136" were used to screen and identify differential expressed genes (DEGs) under the S. fuliginea infection.

Results: There were only 97 DEGs between BK2 and H136 under the control condition, suggesting a similarity in the basal gene expression between the resistant and susceptible cultivated varieties. A large number of hormone signaling-related DEGs (9.2% of all DEGs) between resistant and susceptible varieties were identified, suggesting an involvement of hormone signaling pathways in the resistance to PM. In our study, the defense-related DEGs belonging to Class I were only induced in susceptible cultivated variety and the defense-related DEGs belonging to Class II were only induced in resistant cultivated variety. The peroxidase, NBS, glucanase and chitinase genes that were grouped into Class I and II might contribute to production of the resistance to PM in resistant cultivated variety. Furthermore, several members of Pathogen Response-2 family, such as glucanases and chitinases, were identified as DEGs, suggesting that cucumber might enhance the resistance to PM by accelerating the degradation of the pathogen cell walls. Our data allowed us to identify and analyze more potential genes related to PM resistance.

Keywords: Cucumber; Differential expressed gene; Hormone; Pathogen resistance; Powdery mildew.

Figure 1. Functional KOG classification of all annotated genes in cucumber.

The number of gene belonging the each KOG term was shown. Different colors indicated different categories.

Figure 2. Expression profiles of the differentially expressed genes.

(A) Heat map for cluster analysis of the differentially expressed unigenes by K-means method. Yellow indicates up-regulated genes and blue indicates down-regulated genes. (B) VennDiagrams of the DEGs in different comparisons. (C–N) MeV cluster analysis of differentially expressed genes from the gene expression profiles.

Figure 3. Identification of the DEGs in different comparisons.

(A) Classification of enriched KEGG terms in the DEGs in the RT vs. RC comparison. (B) Classification of enriched KEGG terms in the DEGs in the ST vs. SC comparison.

Figure 4. Identification and differential analysis of the hormonal network in cucumber.

(A) KEGG pathway enrichment analysis of the DEGs showed the top 20 enriched KEGG terms. Rich factor is the proportion of differentially expressed genes in all genes. (B–H) Overview of various hormonal signaling network in cucumber. Red indicated the ST predominantly expressed genes and green indicated the RT predominantly expressed genes.

Figure 5. Identification of classical defense-related DEGs.

(A) Identification of differential expressed NBS genes between the resistant and susceptible cultivated varieties by S. fuliginea infection. (B) Identification of differential expressed glucanase genes between the resistant and susceptible cultivated varieties by S. fuliginea infection. (C) Identification of differential expressed chitinase genes between the resistant and susceptible cultivated varieties by S. fuliginea infection. (D) Identification of differential expressed peroxidase genes between the resistant and susceptible cultivated varieties by S. fuliginea infection. All the up-regulated genes were grouped into the Class I and all down-regulated genes were grouped into the Class II.

Figure 6. Validation of the expression levels of several key genes.

The relative expression levels of eight key genes under the S. fuliginea infection, including GH3 (A), AHP (B), BSK (C), PR1 (D), NBS (E), Peroxidase (F), Glucanase (G), and Chitinase (H). Each bar shows the mean ± SD (n = 3) of triplicates. The significantly changes (P < 0.05) in expression levels of these genes between the treatments and control were indicated by “_”.